Urbanization and the role of urban stormwater runoff as a degrader of streams are well known, but how changes to flow with resulting channel change, impact stream hydraulics is poorly understood. To improve instream habitat for ecosystem health, it is helpful to understand the relative importance of modifying the flow, or modifying the channel. We used two-dimensional (2D) hydrodynamic modelling to compare and contrast the relative effects of channel morphology and flow in setting hydraulic conditions. We explored different test scenarios of urban and natural channel with urban and natural flow and compared them for their habitat value and for its susceptibility to bed movement. Modelling results from the examined scenarios suggest that: 1) both hydrological regime and channel form modification play a key role in altering the instream hydraulics, and 2) for a fundamentally modified channel, addressing just the flow regime is unlikely to restore the hydraulic habitat conditions. This highlights the importance of protecting channels from excess stormwater runoff before geomorphic change occurs, to have a chance of maintaining natural channel hydraulics. Without a natural-like morphology, restoration efforts that only target a natural flow regime are unlikely to achieve appropriate hydraulic conditions, and ecological benefits may thus be unlikely.